What has been done

This section shows the main steps that have been applied to pre-process the raw data.

aCDOM spectra

  • The CDOM spectra were modeled according to the information in Babin 2003.

    • acdom spectra were re-fitted using the complete data (i.e. between 350-500 nm).

  • Average background values calculated between 683-687 nm.

  • Some files were in binary format, so I could not open them (ex.: C2001000.YSA).

  • Some spectra start at 300 nm while others at 350 nm.

  • Calculated the correlation between the measured and the fitted values. Fits with R2 than 0.99 were removed from the data.

  • Exported the complete spectra (350-700 nm): both the raw and the modeled data.

Phytoplankton and non-algal absorption

  • Original data had average background calculated between 745 and 750 nm. This average background have been re-added to the spectra. Thereafter, a new averaged background values were calculated between 746 and 750 nm and subtracted from the spectra.

Irradiance

  • There were negative values in the irradiance data (Ed, Eu, Kd, Ku). I have cleaned the data by setting these negative values to NA.

    • To validate

Other stuff

  • Extracted extra variables (DOC, AQY) from Massimo 2000.

Visualizations

Just some graphs to visualize the data. Note that the same color palette will be used to represent the areas in all graphics.

Geographical map

Available variables

Just an overview of the available variables (excluding radiometric measurements).

Absorption measurements

Overview of the averaged absorption spectra for each area. The acdom spectra have been refitted from the original/raw spectra corrected with the new 746-750 nm background.

Comparing acdom443 for the different areas shows that there is a clear open to coastal gradient.

We can see that the DOC follows the same pattern as acdom443.

We can also use scatterplots to further explore the relationships among variables.

Relationships between some pigments.

TODOS

  • There are two stations without geographical coordinates: C2001000, C2002000.

  • Find a good way to flag the data:

    • For example, all a_phy, a_nap, a_tot spectra contain negative absorption values, but this does not mean they are bad spectra.

  • There are a lot of nutrient parameters that have values of zero. Are they true zero or indicate missing values?

  • Orientation of the paper

    • The data is a mix of temporal and spatial observations, so how should we present the data?

      • By area?

Irradiance data

  • Eu means that Eu0- was estimated (see with Marcel, I do not remember what it means).

  • Ed is Ed0- calculated from 0.96 x ed0+.

    • Change the name in the data files ed to ed0-.

Reflectance

  • There are negative values.

AC9

  • a(715) is always at 0.

  • There are negative values.